Multiple sequence alignment - TraesCS3A01G170100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G170100 chr3A 100.000 4470 0 0 1 4470 178137472 178133003 0.000000e+00 8255.0
1 TraesCS3A01G170100 chr3A 96.449 535 18 1 2 535 679687481 679688015 0.000000e+00 881.0
2 TraesCS3A01G170100 chr3A 95.167 538 23 2 2 536 50932528 50933065 0.000000e+00 846.0
3 TraesCS3A01G170100 chr3A 95.472 530 21 3 3 529 446315787 446316316 0.000000e+00 843.0
4 TraesCS3A01G170100 chr3A 93.443 244 14 2 530 772 178152568 178152326 1.180000e-95 361.0
5 TraesCS3A01G170100 chr3A 86.550 171 18 5 3942 4111 582283374 582283208 2.750000e-42 183.0
6 TraesCS3A01G170100 chr3B 92.501 2307 104 18 1986 4250 223033950 223036229 0.000000e+00 3238.0
7 TraesCS3A01G170100 chr3B 90.916 1244 78 11 711 1931 223032554 223033785 0.000000e+00 1639.0
8 TraesCS3A01G170100 chr3B 95.556 540 22 2 2477 3015 223030205 223029667 0.000000e+00 863.0
9 TraesCS3A01G170100 chr3B 93.182 88 6 0 4236 4323 394954634 394954547 3.630000e-26 130.0
10 TraesCS3A01G170100 chr3B 100.000 58 0 0 1930 1987 223033868 223033925 1.700000e-19 108.0
11 TraesCS3A01G170100 chr3B 87.059 85 11 0 4237 4321 25057526 25057610 3.680000e-16 97.1
12 TraesCS3A01G170100 chr3D 94.652 1870 63 12 1986 3824 152553470 152555333 0.000000e+00 2865.0
13 TraesCS3A01G170100 chr3D 92.595 1283 61 7 732 1987 152552169 152553444 0.000000e+00 1812.0
14 TraesCS3A01G170100 chr3D 89.078 412 27 3 3845 4238 152555329 152555740 3.110000e-136 496.0
15 TraesCS3A01G170100 chr3D 90.446 157 14 1 4314 4470 152555736 152555891 5.860000e-49 206.0
16 TraesCS3A01G170100 chr3D 89.677 155 15 1 3950 4104 288550458 288550611 3.530000e-46 196.0
17 TraesCS3A01G170100 chr3D 83.333 186 25 4 534 714 603431733 603431549 2.770000e-37 167.0
18 TraesCS3A01G170100 chr3D 82.796 186 26 3 533 712 79555098 79555283 1.290000e-35 161.0
19 TraesCS3A01G170100 chr5A 95.669 531 22 1 2 531 705797745 705798275 0.000000e+00 852.0
20 TraesCS3A01G170100 chr5A 95.652 529 21 2 2 528 610722881 610723409 0.000000e+00 848.0
21 TraesCS3A01G170100 chr5A 86.207 174 16 8 3950 4121 86662171 86662004 9.880000e-42 182.0
22 TraesCS3A01G170100 chr5A 84.409 186 22 3 534 712 647359554 647359739 4.600000e-40 176.0
23 TraesCS3A01G170100 chr5A 82.888 187 24 5 534 712 476768504 476768690 1.290000e-35 161.0
24 TraesCS3A01G170100 chr5A 81.818 198 28 5 524 714 648529701 648529505 4.630000e-35 159.0
25 TraesCS3A01G170100 chr7A 95.336 536 24 1 2 536 710707949 710708484 0.000000e+00 850.0
26 TraesCS3A01G170100 chr1A 95.472 530 23 1 2 530 494794216 494794745 0.000000e+00 845.0
27 TraesCS3A01G170100 chr1A 95.113 532 25 1 2 532 472431918 472431387 0.000000e+00 837.0
28 TraesCS3A01G170100 chr2A 94.475 543 26 4 2 541 651460012 651460553 0.000000e+00 833.0
29 TraesCS3A01G170100 chr4D 89.744 156 15 1 3949 4104 74079505 74079351 9.810000e-47 198.0
30 TraesCS3A01G170100 chr7D 89.744 156 13 3 3950 4104 454079230 454079077 3.530000e-46 196.0
31 TraesCS3A01G170100 chr7D 82.979 188 24 7 533 712 595688191 595688004 3.580000e-36 163.0
32 TraesCS3A01G170100 chr7D 88.618 123 14 0 3402 3524 535727908 535728030 2.790000e-32 150.0
33 TraesCS3A01G170100 chr7D 84.270 89 14 0 4236 4324 613328455 613328367 2.220000e-13 87.9
34 TraesCS3A01G170100 chr5B 89.677 155 14 2 3950 4104 299602223 299602375 3.530000e-46 196.0
35 TraesCS3A01G170100 chr5B 83.516 91 13 2 4236 4325 472940351 472940440 2.870000e-12 84.2
36 TraesCS3A01G170100 chr1D 89.677 155 15 1 3950 4104 193504536 193504383 3.530000e-46 196.0
37 TraesCS3A01G170100 chr1D 84.865 185 22 3 534 712 8279644 8279460 9.880000e-42 182.0
38 TraesCS3A01G170100 chr1D 83.784 185 22 4 534 712 58584186 58584004 7.690000e-38 169.0
39 TraesCS3A01G170100 chr1D 89.888 89 8 1 4236 4324 464733218 464733131 3.650000e-21 113.0
40 TraesCS3A01G170100 chr7B 89.431 123 13 0 3402 3524 577563533 577563655 5.990000e-34 156.0
41 TraesCS3A01G170100 chr4A 88.636 88 9 1 4237 4324 585459937 585459851 6.120000e-19 106.0
42 TraesCS3A01G170100 chr4A 86.364 88 12 0 4237 4324 739709872 739709959 3.680000e-16 97.1
43 TraesCS3A01G170100 chr4A 86.364 88 12 0 4237 4324 742105364 742105451 3.680000e-16 97.1
44 TraesCS3A01G170100 chr4A 84.444 90 12 1 4237 4324 739785140 739785051 2.220000e-13 87.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G170100 chr3A 178133003 178137472 4469 True 8255.000000 8255 100.000000 1 4470 1 chr3A.!!$R1 4469
1 TraesCS3A01G170100 chr3A 679687481 679688015 534 False 881.000000 881 96.449000 2 535 1 chr3A.!!$F3 533
2 TraesCS3A01G170100 chr3A 50932528 50933065 537 False 846.000000 846 95.167000 2 536 1 chr3A.!!$F1 534
3 TraesCS3A01G170100 chr3A 446315787 446316316 529 False 843.000000 843 95.472000 3 529 1 chr3A.!!$F2 526
4 TraesCS3A01G170100 chr3B 223032554 223036229 3675 False 1661.666667 3238 94.472333 711 4250 3 chr3B.!!$F2 3539
5 TraesCS3A01G170100 chr3B 223029667 223030205 538 True 863.000000 863 95.556000 2477 3015 1 chr3B.!!$R1 538
6 TraesCS3A01G170100 chr3D 152552169 152555891 3722 False 1344.750000 2865 91.692750 732 4470 4 chr3D.!!$F3 3738
7 TraesCS3A01G170100 chr5A 705797745 705798275 530 False 852.000000 852 95.669000 2 531 1 chr5A.!!$F4 529
8 TraesCS3A01G170100 chr5A 610722881 610723409 528 False 848.000000 848 95.652000 2 528 1 chr5A.!!$F2 526
9 TraesCS3A01G170100 chr7A 710707949 710708484 535 False 850.000000 850 95.336000 2 536 1 chr7A.!!$F1 534
10 TraesCS3A01G170100 chr1A 494794216 494794745 529 False 845.000000 845 95.472000 2 530 1 chr1A.!!$F1 528
11 TraesCS3A01G170100 chr1A 472431387 472431918 531 True 837.000000 837 95.113000 2 532 1 chr1A.!!$R1 530
12 TraesCS3A01G170100 chr2A 651460012 651460553 541 False 833.000000 833 94.475000 2 541 1 chr2A.!!$F1 539

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
610 618 0.037326 CACACACGCACACCCTATCT 60.037 55.0 0.00 0.00 0.00 1.98 F
1404 1435 0.034477 TCAAAGGCGGAATTCTCCCC 60.034 55.0 5.23 3.67 38.71 4.81 F
2146 2307 0.034574 TTCCATGCTGCGGTATTGGT 60.035 50.0 0.00 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 1458 0.601057 CCCAAAATTGTGACCCCGAC 59.399 55.0 0.00 0.00 0.00 4.79 R
3344 3533 1.533625 TAAAGGTGGCATGTCACTGC 58.466 50.0 28.25 13.95 41.53 4.40 R
3798 4013 0.966179 GGTGGTTCCTTTGGCGAATT 59.034 50.0 0.00 0.00 0.00 2.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 105 3.517901 TCGGGAGATTTTCAGCCTTAAGA 59.482 43.478 3.36 0.00 0.00 2.10
350 358 1.890510 GAAAACGGCTGGGTCGTGT 60.891 57.895 0.00 0.00 45.33 4.49
405 413 3.484806 TCGGGGTTGCCACACACT 61.485 61.111 0.00 0.00 0.00 3.55
557 565 5.798015 TTTTTAACACAGTACAGACGCAA 57.202 34.783 0.00 0.00 0.00 4.85
572 580 2.979006 CGCAAGTGCTCATACTTACG 57.021 50.000 1.21 0.00 39.97 3.18
573 581 1.005975 CGCAAGTGCTCATACTTACGC 60.006 52.381 1.21 0.00 39.63 4.42
574 582 1.005975 GCAAGTGCTCATACTTACGCG 60.006 52.381 3.53 3.53 38.78 6.01
575 583 2.259618 CAAGTGCTCATACTTACGCGT 58.740 47.619 19.17 19.17 38.78 6.01
576 584 3.431856 CAAGTGCTCATACTTACGCGTA 58.568 45.455 16.41 16.41 38.78 4.42
577 585 3.984508 AGTGCTCATACTTACGCGTAT 57.015 42.857 21.30 8.84 0.00 3.06
578 586 5.209977 CAAGTGCTCATACTTACGCGTATA 58.790 41.667 21.30 11.02 38.78 1.47
579 587 4.781071 AGTGCTCATACTTACGCGTATAC 58.219 43.478 21.30 8.10 0.00 1.47
580 588 4.274214 AGTGCTCATACTTACGCGTATACA 59.726 41.667 21.30 8.20 0.00 2.29
581 589 5.048921 AGTGCTCATACTTACGCGTATACAT 60.049 40.000 21.30 10.22 0.00 2.29
582 590 5.283247 GTGCTCATACTTACGCGTATACATC 59.717 44.000 21.30 5.67 0.00 3.06
583 591 5.180680 TGCTCATACTTACGCGTATACATCT 59.819 40.000 21.30 0.29 0.00 2.90
584 592 5.508573 GCTCATACTTACGCGTATACATCTG 59.491 44.000 21.30 12.69 0.00 2.90
585 593 6.549912 TCATACTTACGCGTATACATCTGT 57.450 37.500 21.30 12.05 0.00 3.41
586 594 6.368213 TCATACTTACGCGTATACATCTGTG 58.632 40.000 21.30 10.87 0.00 3.66
587 595 4.888038 ACTTACGCGTATACATCTGTGA 57.112 40.909 21.30 0.00 0.00 3.58
588 596 5.239359 ACTTACGCGTATACATCTGTGAA 57.761 39.130 21.30 0.76 0.00 3.18
589 597 5.828747 ACTTACGCGTATACATCTGTGAAT 58.171 37.500 21.30 0.00 0.00 2.57
590 598 5.685954 ACTTACGCGTATACATCTGTGAATG 59.314 40.000 21.30 0.48 0.00 2.67
591 599 2.794910 ACGCGTATACATCTGTGAATGC 59.205 45.455 11.67 0.00 0.00 3.56
592 600 2.794350 CGCGTATACATCTGTGAATGCA 59.206 45.455 0.00 0.00 0.00 3.96
593 601 3.362014 CGCGTATACATCTGTGAATGCAC 60.362 47.826 0.00 0.00 45.35 4.57
601 609 4.210447 GTGAATGCACACACGCAC 57.790 55.556 0.00 0.00 46.56 5.34
602 610 1.354858 GTGAATGCACACACGCACA 59.645 52.632 0.00 0.00 46.56 4.57
603 611 0.929824 GTGAATGCACACACGCACAC 60.930 55.000 0.00 0.00 46.56 3.82
604 612 1.370414 GAATGCACACACGCACACC 60.370 57.895 0.00 0.00 46.56 4.16
605 613 2.731587 GAATGCACACACGCACACCC 62.732 60.000 0.00 0.00 46.56 4.61
606 614 3.772853 ATGCACACACGCACACCCT 62.773 57.895 0.00 0.00 46.56 4.34
607 615 2.280524 GCACACACGCACACCCTA 60.281 61.111 0.00 0.00 0.00 3.53
608 616 1.671054 GCACACACGCACACCCTAT 60.671 57.895 0.00 0.00 0.00 2.57
609 617 1.635663 GCACACACGCACACCCTATC 61.636 60.000 0.00 0.00 0.00 2.08
610 618 0.037326 CACACACGCACACCCTATCT 60.037 55.000 0.00 0.00 0.00 1.98
611 619 0.246635 ACACACGCACACCCTATCTC 59.753 55.000 0.00 0.00 0.00 2.75
612 620 0.532573 CACACGCACACCCTATCTCT 59.467 55.000 0.00 0.00 0.00 3.10
613 621 1.749063 CACACGCACACCCTATCTCTA 59.251 52.381 0.00 0.00 0.00 2.43
614 622 2.362397 CACACGCACACCCTATCTCTAT 59.638 50.000 0.00 0.00 0.00 1.98
615 623 2.362397 ACACGCACACCCTATCTCTATG 59.638 50.000 0.00 0.00 0.00 2.23
616 624 2.623416 CACGCACACCCTATCTCTATGA 59.377 50.000 0.00 0.00 0.00 2.15
617 625 3.068165 CACGCACACCCTATCTCTATGAA 59.932 47.826 0.00 0.00 0.00 2.57
618 626 3.068307 ACGCACACCCTATCTCTATGAAC 59.932 47.826 0.00 0.00 0.00 3.18
619 627 3.068165 CGCACACCCTATCTCTATGAACA 59.932 47.826 0.00 0.00 0.00 3.18
620 628 4.372656 GCACACCCTATCTCTATGAACAC 58.627 47.826 0.00 0.00 0.00 3.32
621 629 4.100189 GCACACCCTATCTCTATGAACACT 59.900 45.833 0.00 0.00 0.00 3.55
622 630 5.395768 GCACACCCTATCTCTATGAACACTT 60.396 44.000 0.00 0.00 0.00 3.16
623 631 6.644347 CACACCCTATCTCTATGAACACTTT 58.356 40.000 0.00 0.00 0.00 2.66
624 632 7.106239 CACACCCTATCTCTATGAACACTTTT 58.894 38.462 0.00 0.00 0.00 2.27
625 633 7.065085 CACACCCTATCTCTATGAACACTTTTG 59.935 40.741 0.00 0.00 0.00 2.44
626 634 7.038302 ACACCCTATCTCTATGAACACTTTTGA 60.038 37.037 0.00 0.00 0.00 2.69
627 635 7.989741 CACCCTATCTCTATGAACACTTTTGAT 59.010 37.037 0.00 0.00 0.00 2.57
628 636 9.213777 ACCCTATCTCTATGAACACTTTTGATA 57.786 33.333 0.00 0.00 0.00 2.15
629 637 9.482627 CCCTATCTCTATGAACACTTTTGATAC 57.517 37.037 0.00 0.00 0.00 2.24
633 641 8.763049 TCTCTATGAACACTTTTGATACACTG 57.237 34.615 0.00 0.00 0.00 3.66
634 642 8.585018 TCTCTATGAACACTTTTGATACACTGA 58.415 33.333 0.00 0.00 0.00 3.41
635 643 8.763049 TCTATGAACACTTTTGATACACTGAG 57.237 34.615 0.00 0.00 0.00 3.35
636 644 5.673337 TGAACACTTTTGATACACTGAGC 57.327 39.130 0.00 0.00 0.00 4.26
637 645 4.515191 TGAACACTTTTGATACACTGAGCC 59.485 41.667 0.00 0.00 0.00 4.70
638 646 3.067106 ACACTTTTGATACACTGAGCCG 58.933 45.455 0.00 0.00 0.00 5.52
639 647 2.416547 CACTTTTGATACACTGAGCCGG 59.583 50.000 0.00 0.00 0.00 6.13
640 648 1.398390 CTTTTGATACACTGAGCCGGC 59.602 52.381 21.89 21.89 0.00 6.13
641 649 0.323302 TTTGATACACTGAGCCGGCA 59.677 50.000 31.54 7.98 0.00 5.69
642 650 0.541392 TTGATACACTGAGCCGGCAT 59.459 50.000 31.54 14.28 0.00 4.40
643 651 1.408969 TGATACACTGAGCCGGCATA 58.591 50.000 31.54 16.21 0.00 3.14
644 652 1.970640 TGATACACTGAGCCGGCATAT 59.029 47.619 31.54 15.25 0.00 1.78
645 653 2.029020 TGATACACTGAGCCGGCATATC 60.029 50.000 31.54 22.20 0.00 1.63
646 654 1.408969 TACACTGAGCCGGCATATCA 58.591 50.000 31.54 22.44 0.00 2.15
647 655 0.761187 ACACTGAGCCGGCATATCAT 59.239 50.000 31.54 6.18 0.00 2.45
648 656 1.270518 ACACTGAGCCGGCATATCATC 60.271 52.381 31.54 16.99 0.00 2.92
649 657 1.001746 CACTGAGCCGGCATATCATCT 59.998 52.381 31.54 4.27 0.00 2.90
650 658 1.696336 ACTGAGCCGGCATATCATCTT 59.304 47.619 31.54 3.33 0.00 2.40
651 659 2.074576 CTGAGCCGGCATATCATCTTG 58.925 52.381 31.54 7.95 0.00 3.02
652 660 1.693606 TGAGCCGGCATATCATCTTGA 59.306 47.619 31.54 0.00 0.00 3.02
653 661 2.289257 TGAGCCGGCATATCATCTTGAG 60.289 50.000 31.54 0.00 0.00 3.02
654 662 1.973515 AGCCGGCATATCATCTTGAGA 59.026 47.619 31.54 0.00 0.00 3.27
655 663 2.570752 AGCCGGCATATCATCTTGAGAT 59.429 45.455 31.54 0.00 34.56 2.75
656 664 3.008813 AGCCGGCATATCATCTTGAGATT 59.991 43.478 31.54 0.00 31.21 2.40
657 665 3.755378 GCCGGCATATCATCTTGAGATTT 59.245 43.478 24.80 0.00 31.21 2.17
658 666 4.937620 GCCGGCATATCATCTTGAGATTTA 59.062 41.667 24.80 0.00 31.21 1.40
659 667 5.163814 GCCGGCATATCATCTTGAGATTTAC 60.164 44.000 24.80 0.00 31.21 2.01
660 668 5.062683 CCGGCATATCATCTTGAGATTTACG 59.937 44.000 0.00 0.00 31.21 3.18
661 669 5.863935 CGGCATATCATCTTGAGATTTACGA 59.136 40.000 0.00 0.00 31.21 3.43
662 670 6.533012 CGGCATATCATCTTGAGATTTACGAT 59.467 38.462 0.00 0.00 31.21 3.73
663 671 7.463780 CGGCATATCATCTTGAGATTTACGATG 60.464 40.741 0.00 0.00 34.33 3.84
664 672 7.332926 GGCATATCATCTTGAGATTTACGATGT 59.667 37.037 0.00 0.00 34.58 3.06
665 673 8.379161 GCATATCATCTTGAGATTTACGATGTC 58.621 37.037 0.00 0.00 34.58 3.06
666 674 9.415544 CATATCATCTTGAGATTTACGATGTCA 57.584 33.333 0.00 0.00 34.58 3.58
667 675 7.706281 ATCATCTTGAGATTTACGATGTCAC 57.294 36.000 0.00 0.00 34.58 3.67
668 676 6.867550 TCATCTTGAGATTTACGATGTCACT 58.132 36.000 0.00 0.00 34.58 3.41
669 677 7.996385 TCATCTTGAGATTTACGATGTCACTA 58.004 34.615 0.00 0.00 34.58 2.74
670 678 8.633561 TCATCTTGAGATTTACGATGTCACTAT 58.366 33.333 0.00 0.00 34.58 2.12
671 679 9.899226 CATCTTGAGATTTACGATGTCACTATA 57.101 33.333 0.00 0.00 31.21 1.31
675 683 8.556517 TGAGATTTACGATGTCACTATAAACG 57.443 34.615 0.00 0.00 0.00 3.60
676 684 7.166970 TGAGATTTACGATGTCACTATAAACGC 59.833 37.037 0.00 0.00 0.00 4.84
677 685 5.954434 TTTACGATGTCACTATAAACGCC 57.046 39.130 0.00 0.00 0.00 5.68
678 686 3.795623 ACGATGTCACTATAAACGCCT 57.204 42.857 0.00 0.00 0.00 5.52
679 687 3.703420 ACGATGTCACTATAAACGCCTC 58.297 45.455 0.00 0.00 0.00 4.70
680 688 3.129813 ACGATGTCACTATAAACGCCTCA 59.870 43.478 0.00 0.00 0.00 3.86
681 689 4.202121 ACGATGTCACTATAAACGCCTCAT 60.202 41.667 0.00 0.00 0.00 2.90
682 690 4.745125 CGATGTCACTATAAACGCCTCATT 59.255 41.667 0.00 0.00 0.00 2.57
683 691 5.234329 CGATGTCACTATAAACGCCTCATTT 59.766 40.000 0.00 0.00 0.00 2.32
684 692 6.238103 CGATGTCACTATAAACGCCTCATTTT 60.238 38.462 0.00 0.00 0.00 1.82
685 693 6.417191 TGTCACTATAAACGCCTCATTTTC 57.583 37.500 0.00 0.00 0.00 2.29
686 694 5.062934 TGTCACTATAAACGCCTCATTTTCG 59.937 40.000 0.00 0.00 0.00 3.46
687 695 5.290158 GTCACTATAAACGCCTCATTTTCGA 59.710 40.000 0.00 0.00 0.00 3.71
688 696 5.290158 TCACTATAAACGCCTCATTTTCGAC 59.710 40.000 0.00 0.00 0.00 4.20
689 697 5.062934 CACTATAAACGCCTCATTTTCGACA 59.937 40.000 0.00 0.00 0.00 4.35
690 698 2.969443 AAACGCCTCATTTTCGACAG 57.031 45.000 0.00 0.00 0.00 3.51
691 699 1.156736 AACGCCTCATTTTCGACAGG 58.843 50.000 0.00 0.00 0.00 4.00
692 700 0.320374 ACGCCTCATTTTCGACAGGA 59.680 50.000 0.00 0.00 0.00 3.86
693 701 1.270625 ACGCCTCATTTTCGACAGGAA 60.271 47.619 0.00 0.00 0.00 3.36
694 702 1.128692 CGCCTCATTTTCGACAGGAAC 59.871 52.381 0.00 0.00 33.42 3.62
695 703 1.128692 GCCTCATTTTCGACAGGAACG 59.871 52.381 0.00 0.00 33.42 3.95
696 704 2.413837 CCTCATTTTCGACAGGAACGT 58.586 47.619 0.00 0.00 33.42 3.99
697 705 2.412089 CCTCATTTTCGACAGGAACGTC 59.588 50.000 0.00 0.00 33.42 4.34
698 706 3.318017 CTCATTTTCGACAGGAACGTCT 58.682 45.455 0.00 0.00 33.42 4.18
699 707 3.314553 TCATTTTCGACAGGAACGTCTC 58.685 45.455 0.00 0.00 33.42 3.36
700 708 2.144482 TTTTCGACAGGAACGTCTCC 57.856 50.000 8.26 8.26 45.81 3.71
707 715 2.979649 GGAACGTCTCCTCCCACC 59.020 66.667 8.87 0.00 41.61 4.61
708 716 2.572284 GAACGTCTCCTCCCACCG 59.428 66.667 0.00 0.00 0.00 4.94
709 717 1.975407 GAACGTCTCCTCCCACCGA 60.975 63.158 0.00 0.00 0.00 4.69
720 728 2.486548 CCTCCCACCGAAAACTTCTTGA 60.487 50.000 0.00 0.00 0.00 3.02
722 730 3.146066 TCCCACCGAAAACTTCTTGATG 58.854 45.455 0.00 0.00 0.00 3.07
777 788 2.965414 CGATTACGTAGCTAAGCACGAG 59.035 50.000 13.40 0.00 36.88 4.18
871 892 5.163447 ACCAATATTTTCTCTCCGTCGATCA 60.163 40.000 0.00 0.00 0.00 2.92
923 944 1.648467 GCGCGCCAATCTTCCTTCTT 61.648 55.000 23.24 0.00 0.00 2.52
935 956 2.415983 TCCTTCTTCTCCTTGACCCA 57.584 50.000 0.00 0.00 0.00 4.51
939 960 4.225267 TCCTTCTTCTCCTTGACCCATAAC 59.775 45.833 0.00 0.00 0.00 1.89
942 963 5.779241 TCTTCTCCTTGACCCATAACAAT 57.221 39.130 0.00 0.00 0.00 2.71
1276 1307 3.551407 GGAGGGAGATGTCGGGGC 61.551 72.222 0.00 0.00 0.00 5.80
1281 1312 3.148279 GAGATGTCGGGGCGAGGT 61.148 66.667 0.00 0.00 36.23 3.85
1363 1394 0.804544 TCGTTGAATGCCGATCGGAC 60.805 55.000 37.64 26.66 37.50 4.79
1374 1405 4.096003 ATCGGACTTGGGCGTGGG 62.096 66.667 0.00 0.00 0.00 4.61
1404 1435 0.034477 TCAAAGGCGGAATTCTCCCC 60.034 55.000 5.23 3.67 38.71 4.81
1568 1615 6.154877 TGTCTTGATCCAAATTGGCATGTATT 59.845 34.615 7.24 0.00 37.47 1.89
1591 1638 1.740025 GCTGTCCTGTTTGATGTAGGC 59.260 52.381 0.00 0.00 0.00 3.93
1602 1649 1.067060 TGATGTAGGCGATGTCCTTCG 59.933 52.381 0.00 0.00 41.99 3.79
1612 1659 0.821517 ATGTCCTTCGGTCGTATGCA 59.178 50.000 0.00 0.00 0.00 3.96
1613 1660 0.604073 TGTCCTTCGGTCGTATGCAA 59.396 50.000 0.00 0.00 0.00 4.08
1629 1676 5.794945 CGTATGCAAGTTGTTTCATTACCAG 59.205 40.000 4.48 0.00 0.00 4.00
1668 1715 9.713740 CAGTTGCTCTATATCAAATCTGAAAAC 57.286 33.333 0.00 0.00 34.49 2.43
1698 1746 2.902608 ACTATGACTGAACCACCCTGA 58.097 47.619 0.00 0.00 0.00 3.86
1700 1748 1.734655 ATGACTGAACCACCCTGACT 58.265 50.000 0.00 0.00 0.00 3.41
1701 1749 2.391926 TGACTGAACCACCCTGACTA 57.608 50.000 0.00 0.00 0.00 2.59
1723 1771 9.477484 GACTATAGATTGTGTAATAAGTGGTGG 57.523 37.037 6.78 0.00 0.00 4.61
1797 1845 1.526225 GCTTCCCCCGGTTAGCATC 60.526 63.158 0.00 0.00 33.88 3.91
1874 1922 5.918608 TGATACAAGATAGTTCTGCCCTTC 58.081 41.667 0.00 0.00 30.72 3.46
1880 1928 5.289083 AGATAGTTCTGCCCTTCTGATTC 57.711 43.478 0.00 0.00 0.00 2.52
1913 1962 8.465999 CCATTTGGCAAATATACAGAAGTAACA 58.534 33.333 23.93 0.00 33.13 2.41
1998 2158 3.444916 CGTACGTTGGCTGAATATGACT 58.555 45.455 7.22 0.00 0.00 3.41
2063 2223 6.072112 AGAATTTTACGTGCACACTCAATT 57.928 33.333 18.64 14.48 0.00 2.32
2098 2259 3.876274 TCAGCTCAAGATTACGAAGCT 57.124 42.857 0.00 0.00 0.00 3.74
2146 2307 0.034574 TTCCATGCTGCGGTATTGGT 60.035 50.000 0.00 0.00 0.00 3.67
2214 2375 6.341316 TCTGATCTTAGTTTCATGTACAGCC 58.659 40.000 0.33 0.00 0.00 4.85
2227 2388 0.107897 TACAGCCGCATTGTACCTGG 60.108 55.000 0.00 0.00 0.00 4.45
2282 2443 8.807118 ACTATGCTGTTGCTTTAGCTATATCTA 58.193 33.333 3.10 0.00 42.66 1.98
2284 2445 8.908786 ATGCTGTTGCTTTAGCTATATCTAAA 57.091 30.769 8.18 8.18 42.66 1.85
2451 2612 5.995897 AGCGGTGAGTAAAGAATTTAGTGTT 59.004 36.000 0.00 0.00 43.82 3.32
2583 2748 4.212214 GGCTATGAGAAGGTGCTATTTTCG 59.788 45.833 0.00 0.00 0.00 3.46
2595 2761 5.051973 GGTGCTATTTTCGTGTTGTTGTTTC 60.052 40.000 0.00 0.00 0.00 2.78
2720 2886 9.831737 CTTCTTTGTACCTCATTTATCTGTTTG 57.168 33.333 0.00 0.00 0.00 2.93
3159 3343 7.767198 CACCCTCATCAAAGAATGCATTAAATT 59.233 33.333 12.97 5.08 0.00 1.82
3238 3422 5.578727 CCAGAGAGTAAGCACACTTGATAAC 59.421 44.000 0.00 0.00 36.57 1.89
3344 3533 3.578716 TCCAGAGTAGACCACTTTTCTGG 59.421 47.826 11.18 11.18 45.86 3.86
3352 3541 1.064758 ACCACTTTTCTGGCAGTGACA 60.065 47.619 15.27 0.00 42.74 3.58
3685 3900 7.976734 ACCTTGATTTTGAAAACAAATGACGTA 59.023 29.630 0.00 0.00 31.63 3.57
3746 3961 2.610433 GCAATGGCTTCCTTTTACTGC 58.390 47.619 0.00 0.00 36.96 4.40
3780 3995 4.229582 TGAATAATAAGCCCCAGGTTCTGT 59.770 41.667 0.00 0.00 34.89 3.41
3781 3996 2.514458 AATAAGCCCCAGGTTCTGTG 57.486 50.000 0.00 0.00 34.89 3.66
3788 4003 0.890996 CCCAGGTTCTGTGGTTCAGC 60.891 60.000 0.00 0.00 43.32 4.26
3840 4056 8.607459 CACCATTGTGATATTCTGAGTAACTTC 58.393 37.037 0.00 0.00 45.76 3.01
3880 4096 1.058748 CAACGCCATTCTACGCACG 59.941 57.895 0.00 0.00 0.00 5.34
3895 4111 1.128507 CGCACGTGTACATCTGCATTT 59.871 47.619 18.38 0.00 0.00 2.32
3965 4193 2.159085 GGTTCTACTCCCTCCATTCACG 60.159 54.545 0.00 0.00 0.00 4.35
3977 4205 5.812642 CCCTCCATTCACGTATATAAGATGC 59.187 44.000 2.47 0.00 0.00 3.91
4026 4254 4.095632 TGCGAACTGAAATGAGTGAACAAA 59.904 37.500 0.00 0.00 0.00 2.83
4044 4272 3.375922 ACAAACACACTAAAACGGGTCTG 59.624 43.478 0.00 0.00 0.00 3.51
4099 4328 7.335627 ACATCTTATAATTTGTGAACGGAGGA 58.664 34.615 0.91 0.00 0.00 3.71
4250 4487 0.033306 GAAGGTACTCCCTCCGTCCT 60.033 60.000 0.00 0.00 45.47 3.85
4251 4488 1.213926 GAAGGTACTCCCTCCGTCCTA 59.786 57.143 0.00 0.00 45.47 2.94
4252 4489 1.532038 AGGTACTCCCTCCGTCCTAT 58.468 55.000 0.00 0.00 40.71 2.57
4253 4490 2.711174 AGGTACTCCCTCCGTCCTATA 58.289 52.381 0.00 0.00 40.71 1.31
4254 4491 3.059097 AGGTACTCCCTCCGTCCTATAA 58.941 50.000 0.00 0.00 40.71 0.98
4255 4492 3.661654 AGGTACTCCCTCCGTCCTATAAT 59.338 47.826 0.00 0.00 40.71 1.28
4256 4493 4.854436 AGGTACTCCCTCCGTCCTATAATA 59.146 45.833 0.00 0.00 40.71 0.98
4257 4494 5.495436 AGGTACTCCCTCCGTCCTATAATAT 59.505 44.000 0.00 0.00 40.71 1.28
4258 4495 6.680197 AGGTACTCCCTCCGTCCTATAATATA 59.320 42.308 0.00 0.00 40.71 0.86
4259 4496 7.185304 AGGTACTCCCTCCGTCCTATAATATAA 59.815 40.741 0.00 0.00 40.71 0.98
4260 4497 7.501892 GGTACTCCCTCCGTCCTATAATATAAG 59.498 44.444 0.00 0.00 0.00 1.73
4261 4498 7.281366 ACTCCCTCCGTCCTATAATATAAGA 57.719 40.000 0.00 0.00 0.00 2.10
4262 4499 7.884891 ACTCCCTCCGTCCTATAATATAAGAT 58.115 38.462 0.00 0.00 0.00 2.40
4263 4500 8.000127 ACTCCCTCCGTCCTATAATATAAGATC 59.000 40.741 0.00 0.00 0.00 2.75
4264 4501 7.879558 TCCCTCCGTCCTATAATATAAGATCA 58.120 38.462 0.00 0.00 0.00 2.92
4265 4502 8.511969 TCCCTCCGTCCTATAATATAAGATCAT 58.488 37.037 0.00 0.00 0.00 2.45
4266 4503 9.148879 CCCTCCGTCCTATAATATAAGATCATT 57.851 37.037 0.00 0.00 0.00 2.57
4297 4534 6.910536 CTATGTTAGCTTGAAAACCGATCT 57.089 37.500 0.00 0.00 0.00 2.75
4298 4535 7.308782 CTATGTTAGCTTGAAAACCGATCTT 57.691 36.000 0.00 0.00 0.00 2.40
4299 4536 8.420374 CTATGTTAGCTTGAAAACCGATCTTA 57.580 34.615 0.00 0.00 0.00 2.10
4300 4537 7.865706 ATGTTAGCTTGAAAACCGATCTTAT 57.134 32.000 0.00 0.00 0.00 1.73
4301 4538 8.958119 ATGTTAGCTTGAAAACCGATCTTATA 57.042 30.769 0.00 0.00 0.00 0.98
4302 4539 8.958119 TGTTAGCTTGAAAACCGATCTTATAT 57.042 30.769 0.00 0.00 0.00 0.86
4303 4540 9.391006 TGTTAGCTTGAAAACCGATCTTATATT 57.609 29.630 0.00 0.00 0.00 1.28
4304 4541 9.651718 GTTAGCTTGAAAACCGATCTTATATTG 57.348 33.333 0.00 0.00 0.00 1.90
4305 4542 7.865706 AGCTTGAAAACCGATCTTATATTGT 57.134 32.000 0.00 0.00 0.00 2.71
4306 4543 7.697691 AGCTTGAAAACCGATCTTATATTGTG 58.302 34.615 0.00 0.00 0.00 3.33
4307 4544 6.912591 GCTTGAAAACCGATCTTATATTGTGG 59.087 38.462 0.00 0.00 0.00 4.17
4308 4545 6.935741 TGAAAACCGATCTTATATTGTGGG 57.064 37.500 0.00 0.00 0.00 4.61
4309 4546 6.654959 TGAAAACCGATCTTATATTGTGGGA 58.345 36.000 0.00 0.00 0.00 4.37
4310 4547 6.540914 TGAAAACCGATCTTATATTGTGGGAC 59.459 38.462 0.00 0.00 0.00 4.46
4311 4548 5.623956 AACCGATCTTATATTGTGGGACA 57.376 39.130 0.00 0.00 0.00 4.02
4312 4549 5.215252 ACCGATCTTATATTGTGGGACAG 57.785 43.478 0.00 0.00 41.80 3.51
4313 4550 4.899457 ACCGATCTTATATTGTGGGACAGA 59.101 41.667 0.00 0.00 41.80 3.41
4314 4551 5.011125 ACCGATCTTATATTGTGGGACAGAG 59.989 44.000 0.00 0.00 41.80 3.35
4315 4552 5.473931 CGATCTTATATTGTGGGACAGAGG 58.526 45.833 0.00 0.00 41.80 3.69
4316 4553 5.567623 CGATCTTATATTGTGGGACAGAGGG 60.568 48.000 0.00 0.00 41.80 4.30
4317 4554 4.890988 TCTTATATTGTGGGACAGAGGGA 58.109 43.478 0.00 0.00 41.80 4.20
4324 4561 2.585900 TGTGGGACAGAGGGAGTAGTAT 59.414 50.000 0.00 0.00 41.80 2.12
4333 4570 9.398538 GGACAGAGGGAGTAGTATATAATGTAG 57.601 40.741 0.00 0.00 0.00 2.74
4359 4596 7.891183 ACTCACATTTCATACTGACAGTTAC 57.109 36.000 14.50 0.00 0.00 2.50
4363 4600 9.337396 TCACATTTCATACTGACAGTTACTTTT 57.663 29.630 14.50 0.00 0.00 2.27
4370 4607 9.151471 TCATACTGACAGTTACTTTTGATAAGC 57.849 33.333 14.50 0.00 0.00 3.09
4373 4610 6.145696 ACTGACAGTTACTTTTGATAAGCGTC 59.854 38.462 1.07 0.00 0.00 5.19
4374 4611 5.118050 TGACAGTTACTTTTGATAAGCGTCG 59.882 40.000 0.00 0.00 0.00 5.12
4451 4688 6.559810 CATACTTGACTACAGAACAGGAGAG 58.440 44.000 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.429822 GCAATTGCCATGCAGAATACACT 60.430 43.478 20.06 0.00 43.29 3.55
12 13 4.821260 TCAGTGTATATTCGCAATTGCCAT 59.179 37.500 24.24 17.94 37.91 4.40
101 105 3.577848 CTCCCGATCTCATCCTTCTCATT 59.422 47.826 0.00 0.00 0.00 2.57
134 139 5.508825 CCCTCCAGAGACGATCATCTAAAAG 60.509 48.000 0.00 0.00 0.00 2.27
388 396 3.484806 AGTGTGTGGCAACCCCGA 61.485 61.111 0.00 0.00 35.87 5.14
422 430 3.013990 CGTTCGCGCGCACAAAAA 61.014 55.556 30.23 14.12 0.00 1.94
459 467 2.261361 CTCGTGTGGCATGGACGA 59.739 61.111 15.52 15.52 39.68 4.20
539 547 3.377439 CACTTGCGTCTGTACTGTGTTA 58.623 45.455 0.00 0.00 0.00 2.41
540 548 2.201732 CACTTGCGTCTGTACTGTGTT 58.798 47.619 0.00 0.00 0.00 3.32
541 549 1.852942 CACTTGCGTCTGTACTGTGT 58.147 50.000 0.00 0.00 0.00 3.72
542 550 0.508641 GCACTTGCGTCTGTACTGTG 59.491 55.000 0.00 0.00 0.00 3.66
543 551 2.900528 GCACTTGCGTCTGTACTGT 58.099 52.632 0.00 0.00 0.00 3.55
554 562 1.005975 CGCGTAAGTATGAGCACTTGC 60.006 52.381 0.00 0.00 39.12 4.01
555 563 2.259618 ACGCGTAAGTATGAGCACTTG 58.740 47.619 11.67 0.00 39.12 3.16
556 564 2.649331 ACGCGTAAGTATGAGCACTT 57.351 45.000 11.67 0.00 41.56 3.16
557 565 3.984508 ATACGCGTAAGTATGAGCACT 57.015 42.857 24.55 0.00 36.10 4.40
558 566 4.530388 TGTATACGCGTAAGTATGAGCAC 58.470 43.478 24.55 9.97 37.80 4.40
559 567 4.816786 TGTATACGCGTAAGTATGAGCA 57.183 40.909 24.55 10.09 37.80 4.26
560 568 5.508573 CAGATGTATACGCGTAAGTATGAGC 59.491 44.000 24.55 7.10 37.80 4.26
561 569 6.520104 CACAGATGTATACGCGTAAGTATGAG 59.480 42.308 24.55 13.58 37.80 2.90
562 570 6.203338 TCACAGATGTATACGCGTAAGTATGA 59.797 38.462 24.55 14.91 37.80 2.15
563 571 6.368213 TCACAGATGTATACGCGTAAGTATG 58.632 40.000 24.55 18.06 37.80 2.39
564 572 6.549912 TCACAGATGTATACGCGTAAGTAT 57.450 37.500 24.55 16.49 40.16 2.12
565 573 5.989551 TCACAGATGTATACGCGTAAGTA 57.010 39.130 24.55 9.40 41.68 2.24
566 574 4.888038 TCACAGATGTATACGCGTAAGT 57.112 40.909 24.55 10.54 41.68 2.24
567 575 5.387444 GCATTCACAGATGTATACGCGTAAG 60.387 44.000 24.55 9.51 43.44 2.34
568 576 4.443063 GCATTCACAGATGTATACGCGTAA 59.557 41.667 24.55 7.41 0.00 3.18
569 577 3.978855 GCATTCACAGATGTATACGCGTA 59.021 43.478 22.94 22.94 0.00 4.42
570 578 2.794910 GCATTCACAGATGTATACGCGT 59.205 45.455 19.17 19.17 0.00 6.01
571 579 2.794350 TGCATTCACAGATGTATACGCG 59.206 45.455 3.53 3.53 0.00 6.01
572 580 4.120646 GTGCATTCACAGATGTATACGC 57.879 45.455 0.00 0.00 42.66 4.42
589 597 2.390306 ATAGGGTGTGCGTGTGTGCA 62.390 55.000 0.00 0.00 43.95 4.57
590 598 1.635663 GATAGGGTGTGCGTGTGTGC 61.636 60.000 0.00 0.00 0.00 4.57
591 599 0.037326 AGATAGGGTGTGCGTGTGTG 60.037 55.000 0.00 0.00 0.00 3.82
592 600 0.246635 GAGATAGGGTGTGCGTGTGT 59.753 55.000 0.00 0.00 0.00 3.72
593 601 0.532573 AGAGATAGGGTGTGCGTGTG 59.467 55.000 0.00 0.00 0.00 3.82
594 602 2.139323 TAGAGATAGGGTGTGCGTGT 57.861 50.000 0.00 0.00 0.00 4.49
595 603 2.623416 TCATAGAGATAGGGTGTGCGTG 59.377 50.000 0.00 0.00 0.00 5.34
596 604 2.945456 TCATAGAGATAGGGTGTGCGT 58.055 47.619 0.00 0.00 0.00 5.24
597 605 3.068165 TGTTCATAGAGATAGGGTGTGCG 59.932 47.826 0.00 0.00 0.00 5.34
598 606 4.100189 AGTGTTCATAGAGATAGGGTGTGC 59.900 45.833 0.00 0.00 0.00 4.57
599 607 5.860941 AGTGTTCATAGAGATAGGGTGTG 57.139 43.478 0.00 0.00 0.00 3.82
600 608 6.875972 AAAGTGTTCATAGAGATAGGGTGT 57.124 37.500 0.00 0.00 0.00 4.16
601 609 7.331026 TCAAAAGTGTTCATAGAGATAGGGTG 58.669 38.462 0.00 0.00 0.00 4.61
602 610 7.496346 TCAAAAGTGTTCATAGAGATAGGGT 57.504 36.000 0.00 0.00 0.00 4.34
603 611 9.482627 GTATCAAAAGTGTTCATAGAGATAGGG 57.517 37.037 0.00 0.00 0.00 3.53
607 615 9.376075 CAGTGTATCAAAAGTGTTCATAGAGAT 57.624 33.333 0.00 0.00 0.00 2.75
608 616 8.585018 TCAGTGTATCAAAAGTGTTCATAGAGA 58.415 33.333 0.00 0.00 0.00 3.10
609 617 8.763049 TCAGTGTATCAAAAGTGTTCATAGAG 57.237 34.615 0.00 0.00 0.00 2.43
610 618 7.331934 GCTCAGTGTATCAAAAGTGTTCATAGA 59.668 37.037 0.00 0.00 0.00 1.98
611 619 7.413438 GGCTCAGTGTATCAAAAGTGTTCATAG 60.413 40.741 0.00 0.00 0.00 2.23
612 620 6.371548 GGCTCAGTGTATCAAAAGTGTTCATA 59.628 38.462 0.00 0.00 0.00 2.15
613 621 5.182001 GGCTCAGTGTATCAAAAGTGTTCAT 59.818 40.000 0.00 0.00 0.00 2.57
614 622 4.515191 GGCTCAGTGTATCAAAAGTGTTCA 59.485 41.667 0.00 0.00 0.00 3.18
615 623 4.377431 CGGCTCAGTGTATCAAAAGTGTTC 60.377 45.833 0.00 0.00 0.00 3.18
616 624 3.498397 CGGCTCAGTGTATCAAAAGTGTT 59.502 43.478 0.00 0.00 0.00 3.32
617 625 3.067106 CGGCTCAGTGTATCAAAAGTGT 58.933 45.455 0.00 0.00 0.00 3.55
618 626 2.416547 CCGGCTCAGTGTATCAAAAGTG 59.583 50.000 0.00 0.00 0.00 3.16
619 627 2.699954 CCGGCTCAGTGTATCAAAAGT 58.300 47.619 0.00 0.00 0.00 2.66
620 628 1.398390 GCCGGCTCAGTGTATCAAAAG 59.602 52.381 22.15 0.00 0.00 2.27
621 629 1.271108 TGCCGGCTCAGTGTATCAAAA 60.271 47.619 29.70 0.00 0.00 2.44
622 630 0.323302 TGCCGGCTCAGTGTATCAAA 59.677 50.000 29.70 0.00 0.00 2.69
623 631 0.541392 ATGCCGGCTCAGTGTATCAA 59.459 50.000 29.70 1.81 0.00 2.57
624 632 1.408969 TATGCCGGCTCAGTGTATCA 58.591 50.000 29.70 2.45 0.00 2.15
625 633 2.029020 TGATATGCCGGCTCAGTGTATC 60.029 50.000 29.70 21.68 0.00 2.24
626 634 1.970640 TGATATGCCGGCTCAGTGTAT 59.029 47.619 29.70 13.38 0.00 2.29
627 635 1.408969 TGATATGCCGGCTCAGTGTA 58.591 50.000 29.70 5.17 0.00 2.90
628 636 0.761187 ATGATATGCCGGCTCAGTGT 59.239 50.000 29.70 9.31 0.00 3.55
629 637 1.001746 AGATGATATGCCGGCTCAGTG 59.998 52.381 29.70 0.00 0.00 3.66
630 638 1.346062 AGATGATATGCCGGCTCAGT 58.654 50.000 29.70 13.44 0.00 3.41
631 639 2.074576 CAAGATGATATGCCGGCTCAG 58.925 52.381 29.70 7.35 0.00 3.35
632 640 1.693606 TCAAGATGATATGCCGGCTCA 59.306 47.619 29.70 23.34 0.00 4.26
633 641 2.028658 TCTCAAGATGATATGCCGGCTC 60.029 50.000 29.70 17.89 0.00 4.70
634 642 1.973515 TCTCAAGATGATATGCCGGCT 59.026 47.619 29.70 15.76 0.00 5.52
635 643 2.462456 TCTCAAGATGATATGCCGGC 57.538 50.000 22.73 22.73 0.00 6.13
636 644 5.062683 CGTAAATCTCAAGATGATATGCCGG 59.937 44.000 0.00 0.00 34.49 6.13
637 645 5.863935 TCGTAAATCTCAAGATGATATGCCG 59.136 40.000 0.00 0.00 34.49 5.69
638 646 7.332926 ACATCGTAAATCTCAAGATGATATGCC 59.667 37.037 10.23 0.00 40.62 4.40
639 647 8.249327 ACATCGTAAATCTCAAGATGATATGC 57.751 34.615 10.23 0.00 40.62 3.14
640 648 9.415544 TGACATCGTAAATCTCAAGATGATATG 57.584 33.333 10.23 0.00 40.62 1.78
641 649 9.416794 GTGACATCGTAAATCTCAAGATGATAT 57.583 33.333 10.23 0.00 40.62 1.63
642 650 8.633561 AGTGACATCGTAAATCTCAAGATGATA 58.366 33.333 10.23 0.00 40.62 2.15
643 651 7.495901 AGTGACATCGTAAATCTCAAGATGAT 58.504 34.615 10.23 0.00 40.62 2.45
644 652 6.867550 AGTGACATCGTAAATCTCAAGATGA 58.132 36.000 10.23 0.00 40.62 2.92
645 653 8.809159 ATAGTGACATCGTAAATCTCAAGATG 57.191 34.615 2.63 2.63 42.95 2.90
649 657 9.016623 CGTTTATAGTGACATCGTAAATCTCAA 57.983 33.333 0.00 0.00 0.00 3.02
650 658 7.166970 GCGTTTATAGTGACATCGTAAATCTCA 59.833 37.037 0.00 0.00 0.00 3.27
651 659 7.358187 GGCGTTTATAGTGACATCGTAAATCTC 60.358 40.741 0.00 0.00 0.00 2.75
652 660 6.420008 GGCGTTTATAGTGACATCGTAAATCT 59.580 38.462 0.00 0.00 0.00 2.40
653 661 6.420008 AGGCGTTTATAGTGACATCGTAAATC 59.580 38.462 0.00 0.00 0.00 2.17
654 662 6.278363 AGGCGTTTATAGTGACATCGTAAAT 58.722 36.000 0.00 0.00 0.00 1.40
655 663 5.653507 AGGCGTTTATAGTGACATCGTAAA 58.346 37.500 0.00 0.00 0.00 2.01
656 664 5.163632 TGAGGCGTTTATAGTGACATCGTAA 60.164 40.000 0.00 0.00 0.00 3.18
657 665 4.336153 TGAGGCGTTTATAGTGACATCGTA 59.664 41.667 0.00 0.00 0.00 3.43
658 666 3.129813 TGAGGCGTTTATAGTGACATCGT 59.870 43.478 0.00 0.00 0.00 3.73
659 667 3.702330 TGAGGCGTTTATAGTGACATCG 58.298 45.455 0.00 0.00 0.00 3.84
660 668 6.604735 AAATGAGGCGTTTATAGTGACATC 57.395 37.500 0.00 0.00 0.00 3.06
661 669 6.238103 CGAAAATGAGGCGTTTATAGTGACAT 60.238 38.462 0.00 0.00 0.00 3.06
662 670 5.062934 CGAAAATGAGGCGTTTATAGTGACA 59.937 40.000 0.00 0.00 0.00 3.58
663 671 5.290158 TCGAAAATGAGGCGTTTATAGTGAC 59.710 40.000 0.00 0.00 0.00 3.67
664 672 5.290158 GTCGAAAATGAGGCGTTTATAGTGA 59.710 40.000 0.00 0.00 0.00 3.41
665 673 5.062934 TGTCGAAAATGAGGCGTTTATAGTG 59.937 40.000 0.00 0.00 0.00 2.74
666 674 5.172934 TGTCGAAAATGAGGCGTTTATAGT 58.827 37.500 0.00 0.00 0.00 2.12
667 675 5.276868 CCTGTCGAAAATGAGGCGTTTATAG 60.277 44.000 0.00 0.00 0.00 1.31
668 676 4.569162 CCTGTCGAAAATGAGGCGTTTATA 59.431 41.667 0.00 0.00 0.00 0.98
669 677 3.374058 CCTGTCGAAAATGAGGCGTTTAT 59.626 43.478 0.00 0.00 0.00 1.40
670 678 2.739913 CCTGTCGAAAATGAGGCGTTTA 59.260 45.455 0.00 0.00 0.00 2.01
671 679 1.535462 CCTGTCGAAAATGAGGCGTTT 59.465 47.619 0.00 0.00 0.00 3.60
672 680 1.156736 CCTGTCGAAAATGAGGCGTT 58.843 50.000 0.00 0.00 0.00 4.84
673 681 0.320374 TCCTGTCGAAAATGAGGCGT 59.680 50.000 0.00 0.00 0.00 5.68
674 682 1.128692 GTTCCTGTCGAAAATGAGGCG 59.871 52.381 0.00 0.00 30.39 5.52
675 683 1.128692 CGTTCCTGTCGAAAATGAGGC 59.871 52.381 0.00 0.00 30.39 4.70
676 684 2.412089 GACGTTCCTGTCGAAAATGAGG 59.588 50.000 0.00 0.00 30.39 3.86
677 685 3.318017 AGACGTTCCTGTCGAAAATGAG 58.682 45.455 0.00 0.00 43.70 2.90
678 686 3.314553 GAGACGTTCCTGTCGAAAATGA 58.685 45.455 0.00 0.00 43.70 2.57
679 687 2.412089 GGAGACGTTCCTGTCGAAAATG 59.588 50.000 8.87 0.00 43.70 2.32
680 688 2.685100 GGAGACGTTCCTGTCGAAAAT 58.315 47.619 8.87 0.00 43.70 1.82
681 689 2.144482 GGAGACGTTCCTGTCGAAAA 57.856 50.000 8.87 0.00 43.70 2.29
682 690 3.879912 GGAGACGTTCCTGTCGAAA 57.120 52.632 8.87 0.00 43.70 3.46
691 699 1.530013 TTCGGTGGGAGGAGACGTTC 61.530 60.000 0.00 0.00 0.00 3.95
692 700 1.117142 TTTCGGTGGGAGGAGACGTT 61.117 55.000 0.00 0.00 0.00 3.99
693 701 1.117142 TTTTCGGTGGGAGGAGACGT 61.117 55.000 0.00 0.00 0.00 4.34
694 702 0.669625 GTTTTCGGTGGGAGGAGACG 60.670 60.000 0.00 0.00 0.00 4.18
695 703 0.685660 AGTTTTCGGTGGGAGGAGAC 59.314 55.000 0.00 0.00 0.00 3.36
696 704 1.346722 GAAGTTTTCGGTGGGAGGAGA 59.653 52.381 0.00 0.00 0.00 3.71
697 705 1.348036 AGAAGTTTTCGGTGGGAGGAG 59.652 52.381 0.00 0.00 34.02 3.69
698 706 1.430992 AGAAGTTTTCGGTGGGAGGA 58.569 50.000 0.00 0.00 34.02 3.71
699 707 1.880027 CAAGAAGTTTTCGGTGGGAGG 59.120 52.381 0.00 0.00 34.02 4.30
700 708 2.846193 TCAAGAAGTTTTCGGTGGGAG 58.154 47.619 0.00 0.00 34.02 4.30
701 709 3.146066 CATCAAGAAGTTTTCGGTGGGA 58.854 45.455 0.00 0.00 34.02 4.37
702 710 2.228822 CCATCAAGAAGTTTTCGGTGGG 59.771 50.000 0.00 0.00 34.02 4.61
703 711 2.884639 ACCATCAAGAAGTTTTCGGTGG 59.115 45.455 0.00 0.00 34.02 4.61
704 712 3.315191 ACACCATCAAGAAGTTTTCGGTG 59.685 43.478 0.00 0.00 46.41 4.94
705 713 3.315191 CACACCATCAAGAAGTTTTCGGT 59.685 43.478 0.00 0.00 34.02 4.69
706 714 3.304659 CCACACCATCAAGAAGTTTTCGG 60.305 47.826 0.00 0.00 34.02 4.30
707 715 3.315191 ACCACACCATCAAGAAGTTTTCG 59.685 43.478 0.00 0.00 34.02 3.46
708 716 4.554723 CGACCACACCATCAAGAAGTTTTC 60.555 45.833 0.00 0.00 0.00 2.29
709 717 3.315191 CGACCACACCATCAAGAAGTTTT 59.685 43.478 0.00 0.00 0.00 2.43
720 728 3.612247 GAGCCTGCGACCACACCAT 62.612 63.158 0.00 0.00 0.00 3.55
739 747 5.389830 CGTAATCGTGGATATTTGATGCTGG 60.390 44.000 0.00 0.00 0.00 4.85
777 788 3.541632 TCCGGAGCTTAATCCATGAAAC 58.458 45.455 0.00 0.00 39.53 2.78
806 827 1.737735 CAGTGCGTCGCTTGATCCA 60.738 57.895 19.50 0.00 0.00 3.41
871 892 2.963320 GGAAACGTGGACGCGTGT 60.963 61.111 20.70 4.97 45.00 4.49
923 944 5.255397 ACAATTGTTATGGGTCAAGGAGA 57.745 39.130 4.92 0.00 0.00 3.71
935 956 5.113383 TCCGCTCGTATCAACAATTGTTAT 58.887 37.500 22.87 17.39 36.32 1.89
939 960 2.930040 ACTCCGCTCGTATCAACAATTG 59.070 45.455 3.24 3.24 0.00 2.32
942 963 1.542472 TCACTCCGCTCGTATCAACAA 59.458 47.619 0.00 0.00 0.00 2.83
1276 1307 5.390567 GCAACACCAAAATTCTACTACCTCG 60.391 44.000 0.00 0.00 0.00 4.63
1281 1312 5.062934 CGATCGCAACACCAAAATTCTACTA 59.937 40.000 0.26 0.00 0.00 1.82
1318 1349 2.480845 GTCGGATCAACTAAATCCCGG 58.519 52.381 0.00 0.00 39.71 5.73
1374 1405 2.513897 CCTTTGATCCCGCCGGTC 60.514 66.667 1.90 0.00 0.00 4.79
1380 1411 0.663153 GAATTCCGCCTTTGATCCCG 59.337 55.000 0.00 0.00 0.00 5.14
1413 1444 3.200593 CGACTGCATCCTGCCAGC 61.201 66.667 0.00 0.00 44.23 4.85
1427 1458 0.601057 CCCAAAATTGTGACCCCGAC 59.399 55.000 0.00 0.00 0.00 4.79
1514 1558 2.036346 ACTGAAAGAAACATTGCAGGGC 59.964 45.455 0.00 0.00 37.43 5.19
1568 1615 2.346766 ACATCAAACAGGACAGCACA 57.653 45.000 0.00 0.00 0.00 4.57
1602 1649 3.889196 TGAAACAACTTGCATACGACC 57.111 42.857 0.00 0.00 0.00 4.79
1612 1659 9.082313 AGAAATCATCTGGTAATGAAACAACTT 57.918 29.630 0.00 0.00 39.04 2.66
1613 1660 8.641498 AGAAATCATCTGGTAATGAAACAACT 57.359 30.769 0.00 0.00 39.04 3.16
1629 1676 4.775236 AGAGCAACTGGGTAGAAATCATC 58.225 43.478 0.00 0.00 0.00 2.92
1668 1715 7.148239 GGTGGTTCAGTCATAGTTAATCCTTTG 60.148 40.741 0.00 0.00 0.00 2.77
1676 1724 4.222145 GTCAGGGTGGTTCAGTCATAGTTA 59.778 45.833 0.00 0.00 0.00 2.24
1689 1737 4.362677 ACACAATCTATAGTCAGGGTGGT 58.637 43.478 0.00 0.00 0.00 4.16
1698 1746 8.989131 ACCACCACTTATTACACAATCTATAGT 58.011 33.333 0.00 0.00 0.00 2.12
1797 1845 4.082274 TGTTGTGCTAAGAAATGCATCG 57.918 40.909 0.00 0.00 41.45 3.84
1856 1904 4.478206 TCAGAAGGGCAGAACTATCTTG 57.522 45.455 0.00 0.00 32.03 3.02
1874 1922 3.196039 TGCCAAATGGTCAATGGAATCAG 59.804 43.478 0.71 0.00 36.27 2.90
1880 1928 6.580788 TGTATATTTGCCAAATGGTCAATGG 58.419 36.000 12.86 0.00 37.57 3.16
2059 2219 9.467258 TGAGCTGAAAACAGAAATAGAAAATTG 57.533 29.630 0.00 0.00 0.00 2.32
2063 2223 8.450578 TCTTGAGCTGAAAACAGAAATAGAAA 57.549 30.769 0.00 0.00 0.00 2.52
2146 2307 3.585289 TCACTTACAGAAACCAGCCCATA 59.415 43.478 0.00 0.00 0.00 2.74
2187 2348 7.010923 GCTGTACATGAAACTAAGATCAGAAGG 59.989 40.741 0.00 0.00 0.00 3.46
2214 2375 6.146184 CAGAGTAATTATCCAGGTACAATGCG 59.854 42.308 0.00 0.00 0.00 4.73
2451 2612 3.287222 AGCAAGGCTTGTTGTTAACTCA 58.713 40.909 26.71 3.74 33.89 3.41
2558 2723 5.379706 AAATAGCACCTTCTCATAGCCTT 57.620 39.130 0.00 0.00 0.00 4.35
2583 2748 3.670991 TCAAAACGCAGAAACAACAACAC 59.329 39.130 0.00 0.00 0.00 3.32
2595 2761 7.616673 TGTCATAAAAACATTTCAAAACGCAG 58.383 30.769 0.00 0.00 0.00 5.18
2690 2856 9.219603 CAGATAAATGAGGTACAAAGAAGACAA 57.780 33.333 0.00 0.00 0.00 3.18
2720 2886 9.516314 GGTTTTCTGGTATAATATTGTTTCTGC 57.484 33.333 0.00 0.00 0.00 4.26
2812 2978 7.149569 ACATGATCCAAACTTACACATGAAG 57.850 36.000 0.00 0.00 37.59 3.02
3159 3343 5.567037 ACCCTAGCTGCATATATGTCAAA 57.433 39.130 14.14 0.00 0.00 2.69
3238 3422 3.690628 TGACACTACCATCATGCATGTTG 59.309 43.478 25.43 25.06 0.00 3.33
3295 3484 5.877012 TCACCAGAAGATTTCTACATGAAGC 59.123 40.000 0.00 0.00 38.11 3.86
3344 3533 1.533625 TAAAGGTGGCATGTCACTGC 58.466 50.000 28.25 13.95 41.53 4.40
3352 3541 8.156165 TCAGAATTTGAAAAATAAAGGTGGCAT 58.844 29.630 0.00 0.00 31.34 4.40
3383 3572 6.939730 TGTTACAGCAAATGGTTCTCATTAGA 59.060 34.615 0.00 0.00 44.68 2.10
3746 3961 7.939039 TGGGGCTTATTATTCAGAAGATAAGTG 59.061 37.037 20.06 7.11 35.52 3.16
3798 4013 0.966179 GGTGGTTCCTTTGGCGAATT 59.034 50.000 0.00 0.00 0.00 2.17
4026 4254 2.994186 ACAGACCCGTTTTAGTGTGT 57.006 45.000 0.00 0.00 35.82 3.72
4099 4328 5.148651 ACAAGGAAGCGTAGAATGTACTT 57.851 39.130 0.00 0.00 0.00 2.24
4148 4380 7.663493 AGTTCTCTTTATCCTTGAACCAGAAAG 59.337 37.037 0.00 0.00 38.10 2.62
4160 4392 6.059787 AGACATGCAAGTTCTCTTTATCCT 57.940 37.500 0.00 0.00 0.00 3.24
4274 4511 6.910536 AGATCGGTTTTCAAGCTAACATAG 57.089 37.500 0.00 0.00 0.00 2.23
4275 4512 8.958119 ATAAGATCGGTTTTCAAGCTAACATA 57.042 30.769 0.00 0.00 0.00 2.29
4276 4513 7.865706 ATAAGATCGGTTTTCAAGCTAACAT 57.134 32.000 0.00 0.00 0.00 2.71
4277 4514 8.958119 ATATAAGATCGGTTTTCAAGCTAACA 57.042 30.769 0.00 0.00 0.00 2.41
4278 4515 9.651718 CAATATAAGATCGGTTTTCAAGCTAAC 57.348 33.333 0.00 0.00 0.00 2.34
4279 4516 9.391006 ACAATATAAGATCGGTTTTCAAGCTAA 57.609 29.630 0.00 0.00 0.00 3.09
4280 4517 8.826710 CACAATATAAGATCGGTTTTCAAGCTA 58.173 33.333 0.00 0.00 0.00 3.32
4281 4518 7.201732 CCACAATATAAGATCGGTTTTCAAGCT 60.202 37.037 0.00 0.00 0.00 3.74
4282 4519 6.912591 CCACAATATAAGATCGGTTTTCAAGC 59.087 38.462 0.00 0.00 0.00 4.01
4283 4520 7.282224 TCCCACAATATAAGATCGGTTTTCAAG 59.718 37.037 0.00 0.00 0.00 3.02
4284 4521 7.066525 GTCCCACAATATAAGATCGGTTTTCAA 59.933 37.037 0.00 0.00 0.00 2.69
4285 4522 6.540914 GTCCCACAATATAAGATCGGTTTTCA 59.459 38.462 0.00 0.00 0.00 2.69
4286 4523 6.540914 TGTCCCACAATATAAGATCGGTTTTC 59.459 38.462 0.00 0.00 0.00 2.29
4287 4524 6.419791 TGTCCCACAATATAAGATCGGTTTT 58.580 36.000 0.00 0.00 0.00 2.43
4288 4525 5.996644 TGTCCCACAATATAAGATCGGTTT 58.003 37.500 0.00 0.00 0.00 3.27
4289 4526 5.365605 TCTGTCCCACAATATAAGATCGGTT 59.634 40.000 0.00 0.00 0.00 4.44
4290 4527 4.899457 TCTGTCCCACAATATAAGATCGGT 59.101 41.667 0.00 0.00 0.00 4.69
4291 4528 5.468540 TCTGTCCCACAATATAAGATCGG 57.531 43.478 0.00 0.00 0.00 4.18
4292 4529 5.473931 CCTCTGTCCCACAATATAAGATCG 58.526 45.833 0.00 0.00 0.00 3.69
4293 4530 5.544176 TCCCTCTGTCCCACAATATAAGATC 59.456 44.000 0.00 0.00 0.00 2.75
4294 4531 5.476983 TCCCTCTGTCCCACAATATAAGAT 58.523 41.667 0.00 0.00 0.00 2.40
4295 4532 4.890988 TCCCTCTGTCCCACAATATAAGA 58.109 43.478 0.00 0.00 0.00 2.10
4296 4533 4.656112 ACTCCCTCTGTCCCACAATATAAG 59.344 45.833 0.00 0.00 0.00 1.73
4297 4534 4.631234 ACTCCCTCTGTCCCACAATATAA 58.369 43.478 0.00 0.00 0.00 0.98
4298 4535 4.280789 ACTCCCTCTGTCCCACAATATA 57.719 45.455 0.00 0.00 0.00 0.86
4299 4536 3.136641 ACTCCCTCTGTCCCACAATAT 57.863 47.619 0.00 0.00 0.00 1.28
4300 4537 2.642171 ACTCCCTCTGTCCCACAATA 57.358 50.000 0.00 0.00 0.00 1.90
4301 4538 2.225650 ACTACTCCCTCTGTCCCACAAT 60.226 50.000 0.00 0.00 0.00 2.71
4302 4539 1.149288 ACTACTCCCTCTGTCCCACAA 59.851 52.381 0.00 0.00 0.00 3.33
4303 4540 0.784495 ACTACTCCCTCTGTCCCACA 59.216 55.000 0.00 0.00 0.00 4.17
4304 4541 2.822707 TACTACTCCCTCTGTCCCAC 57.177 55.000 0.00 0.00 0.00 4.61
4305 4542 6.791847 TTATATACTACTCCCTCTGTCCCA 57.208 41.667 0.00 0.00 0.00 4.37
4306 4543 7.183460 ACATTATATACTACTCCCTCTGTCCC 58.817 42.308 0.00 0.00 0.00 4.46
4307 4544 9.398538 CTACATTATATACTACTCCCTCTGTCC 57.601 40.741 0.00 0.00 0.00 4.02
4308 4545 9.962809 ACTACATTATATACTACTCCCTCTGTC 57.037 37.037 0.00 0.00 0.00 3.51
4359 4596 4.232641 GTCAGTCGACGCTTATCAAAAG 57.767 45.455 10.46 0.00 31.07 2.27
4373 4610 3.058914 CCTGCAAACCTTTTAGTCAGTCG 60.059 47.826 0.00 0.00 0.00 4.18
4374 4611 4.134563 TCCTGCAAACCTTTTAGTCAGTC 58.865 43.478 0.00 0.00 0.00 3.51
4421 4658 7.602644 CCTGTTCTGTAGTCAAGTATGCTTTTA 59.397 37.037 0.00 0.00 31.49 1.52
4425 4662 4.772624 TCCTGTTCTGTAGTCAAGTATGCT 59.227 41.667 0.00 0.00 0.00 3.79
4426 4663 5.073311 TCCTGTTCTGTAGTCAAGTATGC 57.927 43.478 0.00 0.00 0.00 3.14
4427 4664 6.375736 TCTCTCCTGTTCTGTAGTCAAGTATG 59.624 42.308 0.00 0.00 0.00 2.39
4428 4665 6.486056 TCTCTCCTGTTCTGTAGTCAAGTAT 58.514 40.000 0.00 0.00 0.00 2.12
4435 4672 3.829601 CCTGTTCTCTCCTGTTCTGTAGT 59.170 47.826 0.00 0.00 0.00 2.73


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.